The National Party is accusing Associate Transport Minister Julie Anne Genter of gagging New Zealanders opposed to the car tax-rebate scheme.
Ms Genter launched a consultation process on 9 July for a proposal that would apply charges or subsidies on new and used car imports depending on their emissions profile.
National leader Simon Bridges said 1000 of the 1500 submissions delivered via the party's website have been discarded because the Ministry of Transport deemed them spam.
"I would not in government be criticising Labour, the Greens or New Zealand First for mobilising people and making it convenient for them to have their say. That's what we've done here, now we've clearly come at it from a certain viewpoint,'' he said.
In official documents the Ministry of Transport said it received 500 emails from the same email address opposing the Clean Car Discount, and subsequently the ministry blocked any further emails from that address.
Neither the ministry nor the National Party could confirm that the email address set up by the opposition was the email in question but Mr Bridges said it's likely it was because the summary of the results by the ministry said the policy had overwhelming support.
If the 1500 submissions from the National Party website had been included the support for the policy would be much different, he said.
The National Party's submission form allowed submitters to customise their response or use the automatic one set up by the party but each submitter had to provide their own email address as a point of contact.
A total of 1594 people made formal submissions on the proposal through National's website while another 14,060 people signed a petition to stop Labour's car tax.
But Ms Genter said the National Party petition included claims about the policy, which the Advertising Standards Authority has since ruled to be misleading.
She said she's asked the ministry to clarify on Monday whether the emails in question came from the National Party and "whether they resemble an online form submission''.
"The Ministry of Transport advised that during consultation they received over 500 emails from a single digital signature. I am told the ministry classified these emails as spam as they contained the same message and were received consecutively over a very short period of time.
"Ministry officials then made the decision to consider the emails as one individual submission,'' she said.
But Mr Bridges insists it's a "non-genuine consultation process that blocks certain views''.
He said where the ministry received block submissions they agreed with, from Greenpeace for example, they counted them but have not in this case.
"They might not be quite at the level of formal organisations submitting like the AA or the Motorvehicle Association but they're still valid, they're still New Zealanders who have got a view and not to count them is an affront to democracy,'' he said.